Ascent: An Agentic System over the Model Context Protocol for Real-World Clinical Data Analysis

Objective: To develop and characterize CLEAR-Med, a dual-agent framework for natural-language analysis of structured clinical data that separates SQL-based invocation from independent validation. Methods: CLEAR-Med uses one agent to translate a question into executable Structured Query Language (SQL), retain the executed query and database result, and produce a draft. Deterministic checks and a separately invoked cross-provider Validation Agent then accept the draft, request one bounded repair, or abstain. We formalized the system as a bounded selective pipeline and evaluated CLEAR-Med's configuration and scalability, and the Invocation Agent's accuracy and consistency on a 25-query development benchmark, using a harmonized 21-site neonatal hypoxic-ischemic encephalopathy table containing 532 de-identified infant records and approximately 1,300 variables. Results: CLEAR-Med completed all six nominal scalability configurations, including 500x1300. Across 25 development-benchmark queries repeated five times, the Invocation Agent answered 83 of 125 responses correctly (66.4%; query-cluster bootstrap 95% CI, 48.0-83.2%), compared with 15 of 125 (12.0%; 95% CI, 3.2-22.4%) for the ungrounded ChatGPT baseline, a paired improvement of 54.4 percentage points (95% CI, 36.8-72.0%). Conclusion: CLEAR-Med provides a general architecture for traceable analysis of structured clinical data: numerical claims remain linked to executed SQL, and unresolved cases can fail closed. The reported experiments characterize CLEAR-Med's configuration and scalability and the Invocation Agent's accuracy, while the formal analysis establishes the encoded-property guarantee of the complete control flow; a prospective full-pipeline evaluation of the validation and abstention stages is the next stage of this work.

Clinical data-science agents must transform heterogeneous longitudinal records into auditable analyses, yet existing benchmarks largely isolate medical question answering, structured-table reasoning, or generic scientific repositories. We introduce CLINLENS, a benchmark of 200 executable tasks over five linked MIMIC resources spanning structured electronic health records, notes, electrocardiograms, chest radiographs, and echocardiograms. A 4 x 5 taxonomy crosses four patient-time scopes with five analysis capabilities. Program-first reverse synthesis pairs each bounded semi-raw package with an evaluator-private reference workflow and checks required artifacts, cohort and temporal semantics, and the final answer. On a fixed 126-task suite, the strongest of 24 standardized model-scaffold configurations achieves 56.3% scope-macro STRICTPASS despite 100% EXECSUCCESS. For reference, a separately configured coding agent solves 83 of 126 tasks, while five biomedical systems adapted to GPT-4o-mini reach at most 2.9% scope-macro STRICTPASS. These results expose a substantial gap between runnable submissions and correct clinical analyses.

We introduce PhysicianBench, a benchmark for evaluating LLM agents on physician tasks grounded in real clinical setting within electronic health record (EHR) environments. Existing medical agent benchmarks primarily focus on static knowledge recall, single-step atomic actions, or action intent without verifiable execution against the environment. As a result, they fail to capture the long-horizon, composite workflows that characterize real clinical systems. PhysicianBench comprises 100 long-horizon tasks adapted from real consultation cases between primary care and subspecialty physicians, with each task independently reviewed by a separate panel of physicians. Tasks are instantiated in an EHR environment with real patient records and accessed through the same standard APIs used by commercial EHR vendors. Tasks span 21 specialties (e.g., cardiology, endocrinology, oncology, psychiatry) and diverse workflow types (e.g., diagnosis interpretation, medication prescribing, treatment planning), requiring an average of 27 tool calls per task. Solving each task requires retrieving data across encounters, reasoning over heterogeneous clinical information, executing consequential clinical actions, and producing clinical documentation. Each task is decomposed into structured checkpoints (670 in total across the benchmark) capturing distinct stages of completion graded by task-specific scripts with execution-grounded verification. Across 13 proprietary and open-source LLM agents, the best-performing model achieves only 46% success rate (pass@1), while open-source models reach at most 19%, revealing a substantial gap between current agent capabilities and the demands of real-world clinical workflows. PhysicianBench provides a realistic and execution-grounded benchmark for measuring progress toward autonomous clinical agents.